Gene expression analysis of M. tuberculosis in patients with and without HIV co-infection

Group 3: Anne Skov-Johannessen s184330, Dea F. Skipper, Helene B. L. Petersen s194699, Johanne B. Overgaard s194691 and Rebecca C. Grenov

Introduction

The leading cause of death in HIV-infected individuals.

  • Weakened immune system

  • Limits sensitivity of diagnosis of TB

Support vector machine to find 251-gene signature

  • Genes involved in Immunological, Infectious and Inflammatory Disease

  • Limits sensitivity of diagnosis of TB

Our aim:

  • Explore genes with a significant expression enriched in HIV with TB co-infection

  • Compare with the 251-gene signature found with the SVM model

Method

Data handling:

  • Select variables

  • Mutate variables

  • Handle key-variable

  • Handle replications

Methods

Methods

Normalization Log2

Methods

Results - PCA

  • First PC explains 15% of the variance

  • 31 PCs needed to explain 90% of variance

Results - PCA

  • Slight partition of disease state on PC1
  • No clear partition of gender

Results - Linear Regression

Forest plot

Results - Linear Regression

Volcano plot